Graduate Courses

EN.540.601. Chemical and Biomolecular Engineering Seminar. 1.00 Credit.

Instructor: S. Jeong
Area: Engineering

EN.540.602. Metabolic Systems Biotechnology. 3.00 Credits.

The aim of this course is to provide a fundamental understanding of the quantitative principles and methodologies of systems biology and biochemical engineering of metabolism. This includes concepts of cellular growth, cellular stoichiometric models, metabolic networks, metabolite fluxes, and genome-scale metabolic models. Quantitative methods and systems biology approaches for metabolic flux analysis and metabolic control theory will be included as well as an analysis of biochemical systems and bioreactors including a consideration of mass transport processes.
Instructor: M. Betenbaugh
Area: Engineering.

EN.540.603. Colloids and Nanoparticles. 3.00 Credits.

Fundamental principles related to interactions, dynamics, and structure in colloidal, nanoparticle, and interfacial systems. Concepts covered include hdrodynamics, Brownian motion, diffusion, sedimentation, electrophoresis, colloidal and surface forces, polymeric forces, aggregation, deposition, and experimental methods. Modern topics related to colloids in nano- science and technology will be discussed throughout the course with frequent references to recent literature. Meets with EN.540.403
Instructor: M. Bevan
Area: Engineering

EN.540.605. The Design of Biomolecular Systems. 3.00 Credits.

This course covers new topics in the design of systems of biomolecules, both in vitro and in vivo, for decision making and control. The course will begin with an overview of how logical decision making and control with biomolecules as is achieved in biology and then proceed to consider various strategies of engineering similar systems. The focus of the course will be on systems level principles rather than the biochemistry of molecule design. Topics will include engineering of transcriptional networks and genetic control for logically programming of cells, the design of in vitro mimics of genetic controls, molecular computing and systems aspects of metabolic engineering. The course will also cover quantitative and computational techniques for the simulation and analysis of biomolecular systems. Co-listed with EN.540.405
Instructor: R. Schulman
Area: Engineering

EN.540.606. Chemical & Biomolecular Separation. 3.00 Credits.

This course covers staged and continuous-contacting separations processes critical to the chemical and biochemical industries. Separations technologies studied include distillation, liquid-liquid extraction, gas absorption, membrane ultrafiltration, reverse osmosis, dialysis, adsorption, and chromatography. Particular emphasis is placed on the biochemical uses of these processes and consequently on how the treatment of these processes differs from the more traditional approach. Only with permission of the instructor. Co-listed with EN.540.306
Instructor: M. Betenbaugh
Area: Engineering

EN.540.407/540.607/545.607. Renewable Energy Technologies: A Chemical Engineering Perspective. 3.00 credits.

In this ChemBE course we discuss the principles governing renewable energy technologies, with an emphasis on the fundamental mechanisms from a chemical engineering perspective. Lectures will first be given to introduce state-of-the-art renewable energy technologies, including carbon capture and utilization, solar cells/photovoltaics, batteries, fuel cells/electrolyzers, biomass/biofuels, etc. Discussions will then be carried out to interpret the thermodynamic, kinetic and transport processes governing the energy conversion efficiencies and power performance of such systems. The technical understanding will be followed up with tech-economic and/or life-cycle assessments to evaluate the scalability, commercial viability and environmental sustainability of each technology. Our discussion will be accompanied with reading, survey and presentation of renewable energy research literature with topics identified through group discussions. The final project of the class will be an essay to introduce a technology of interest. Co-listed with EN.540.407.
Instructor: C. Wang. Syllabus
Area: Engineering

EN.540.610. Chemical and Biomolecular Engineering Design: Spring. 3.00 Credits.

This course is one part of a two semester sequence. This course guides the student through the contrasting aspects of product design and of process design. Product design concerns the recognition of customer needs, the creation of suitable specifications, and the selection of best products to fulfill the needs. Process design concerns the quantitative description of processes which serve to produce many commodity chemicals, the estimation of process profitability, and the potential for profitability improvement through incremental changes in the process. Students work in small teams to complete a major project demonstrating their understanding of and proficiency in the primary objectives of the course. Students report several times both orally and in writing on their accomplishments. Laboratory tests can be performed and/or prototypes can be made. Note that both courses, 540.609 and 540.610 must be taken, the two courses can be started in any term.
Instructor: M. Donohue
Area: Engineering

EN.540.614. Computational Protein Structure Prediction and Design. 3.00 Credits.

This class will introduce the fundamental concepts in protein structure, biophysics, optimization and informatics that have enabled the breakthroughs in computational structure prediction and design. Problems covered will include protein folding and docking, design of ligand-binding sites, design of turns and folds, design of protein interfaces. Class will consist of lectures and hands-on computer workshops. Students will learn to use molecular visualization tools and write programs with the PyRosetta protein structure software suite, including a computational project. Programming experience is recommended.
Instructor: J. Gray
Area: Engineering

EN.540.615. Interfacial Science with Applications to Nanoscale Systems. 3.00 Credits.

Nanostructured materials intrinsically possess large surface area (interface area) to volume ratios. It is this large interfacial area that gives rise to many of the amazing properties and technologies associated with nanotechnology. In this class we will examine how the properties of surfaces, interfaces, and nanoscale features differ from their macroscopic behavior. We will compare and contrast fluid-fluid interfaces with solid-fluid and solid-solid interfaces, discussing fundamental interfacial physics and chemistry, as well as touching on state-of-the-art technologies.
Instructor(s): TBA
Area: Engineering

EN.540.618: Metabolic Dysfunctions and Related Diseases

EN.540.619. Projects in Design: Alternative Energy. 3.00 Credits.

This course is a group design project (i.e. not a lecture course) to use chemical process simulation tools to model a real-world, alternative-energy process of interest to Chemical and Biomolecular Engineers. The goal of the project will be to develop a process model that is sufficiently complete and robust that it can be used to understand the important factors in the process design and/or operation. This design project is focused on the role alternative energy will play in our country’s future. About a third of the course will be devoted to understanding the role of energy and alternative energy in the US and world economies. The remainder of the course will be devoted to a technical and economic analysis of an alternative energy technology. This course is organized to replicate group project work as it is practiced in industry. The class is divided into groups (typically 3 or 4 students) and each group will meet separately each week with the instructor. Hence, there is no regularly scheduled class times; student groups sign up for weekly meeting times using Starfish in Blackboard. These meetings typically will be 60 minutes long. The expectations and assignments for this course are quite different from most other courses. There are no weekly lectures by the instructor. Rather, each week each group will make a PowerPoint presentation on the week’s topic or their progress on their project. Graduate level. Meets with EN.540.401
Prerequisites: EN.540.202 AND EN.540.203 AND EN.540.301 AND EN.540.305
Instructor: M. Donohue
Area: Engineering

EN.540.621. Project in Design: Pharmacodynamics. 3.00 Credits.

This course covers pharmacodynamics, i.e. how pharmaceuticals affect biological processes. The course will use MatLab to aid in the design of new drug formulations.
Instructor: M. Donohue
Area: Engineering, Natural Sciences

EN.540.622. Introduction to Polymeric Materials. 3.00 Credits.

Polymeric materials are ubiquitous in our society from Nature-made proteins and polysaccharides to synthetic plastics and fibers. Their applications range from day-to-day consumables to high performance materials used in critically demanding areas, such as aviation, aerospace and medical devices. The objective of this course is to provide an introductory overview on the field of polymer science and engineering. Students will learn some basic concepts in polymer synthesis, characterization, and processing. With the basic concepts established, industrial applications of polymeric materials will be discussed in two categories: structural polymers and functional polymers. Structural polymers, including plastics, fibers, rubbers, coatings, adhesives, and composites, will be discussed in terms of their structure, processing, and property relationship with a flavor of industrial relevant products and applications. Future trends in developing environmentally friendly polymers from renewable resources (“green polymer chemistry”) will also be covered. Lectures on functional polymers will be focused on their unique properties that are enabled by rational molecular design, controlled synthesis and processing (e.g. supramolecular assembly, and microfabrication). This class of specialty materials can find their use in high performance photovoltaics, batteries, membranes, and composites, and can also serve as “smart” materials for use in coatings, sensors, medical devices, and biomimicry.
Instructor(s): H. Cui; K. Qi
Area: Engineering

EN.540.628. Supramolecular Materials and Nanomedicine. 3.00 Credits.

Nanomedicine is a quickly growing area that exploits the novel chemical, physical, and biological properties of nanostructures and nanostructured materials for medical treatments. This course presents basic design principles of constructing nanomaterials for use in drug delivery, disease diagnosis and imaging, and tissue engineering. Three major topics will be discussed, including 1) nanocarriers for drug delivery that are formed through soft matter assembly (e.g., surfactants, lipids, block copolymers, DNA, polyelectrolytes, peptides), 2) inorganic nanostructures for disease diagnosis and imaging (e.g., nanoparticles of gold and silver, quantum dots and carbon nanotubes), and 3) supramolecular scaffolds for tissue engineering and regenerative medicine. Students are expected to learn the physical, chemical and biological properties of each nanomaterial, the underlying physics and chemistry of fabricating such material, as well as their advantages and potential issues when used for biomedical applications. This course will also provide students opportunities for case studies on commercialized nanomedicine products. After this class, students should gain a deeper understanding of current challenges in translating nanoscience and nanotechnology into medical therapies.
Instructor: H. Cui
Area: Engineering, Natural Sciences

EN.540.630. Thermodynamics, Statistical Mechanics, and Kinetics. 3.00 Credits.

In this course we will aim for understanding the thermodynamics of chemical and bio-molecular systems. We will first review classical, macroscopic thermodynamics covering concepts such as equilibrium, stability and the role of thermodynamic potentials. Our goal will be to gain a feel for the generality of thermodynamics. Statistical mechanics provides a link between the mechanics of atoms and macroscopic thermodynamics. We will introduce this branch in two distinct ways: 1) following standard methods of developing concepts such as ensembles and partition functions, and 2) where we will treat the basis of statistical mechanics as a problem in inference. With this foundation, we will consider concepts relevant to understanding the liquid state. Chemical transformations in a liquid are of importance in much of chemistry and biology; quasi-chemical generalizations of the potential distribution theorem will be introduced to present these ideas. We hope to give an overview of modern developments relating equilibrium work to non-equilibrium work, as these are of increasing importance in studies on single molecule systems. Registration by instructor permission only.
Instructor: C. Wang
Area: Engineering

EN.540.632. Project in Design: Pharmacokinetics. 3.00 Credits.

This is a design course in which the design projects will be to develop pharmacokinetic models of the human body that can be used to understand the temporal distribution, spatial distribution and bioavailability of pharmaceutical drugs. The course (and software to be developed) will cover the spectrum of factors affecting pharmaceutical bioavailability including drug formulation, mode of dosing and dosing rate, metabolism and metabolic cascades, storage in fatty tissues, and diffusional limitations (such as in crossing the blood-brain barrier or diffusional differences between normal and cancerous cells). The goal is to develop process models of the human body that will predict pharmaceutical bioavailability as a function of time and organ (or cell) type that will work for a wide variety of pharmaceuticals including small molecules, biologics, and chemotherapy agents. This course is organized to replicate group project work as it is practiced in industry. The class is divided into groups (typically 3 or 4 students) and each group will meet separately each week with the instructor. Hence, there is no regularly scheduled class times; student groups sign up for weekly meeting times using Starfish in Blackboard. These meetings typically will be 90 minutes long. The expectations and assignments for this course are quite different from most other courses. There are no weekly lectures by the instructor. Rather, each week each group will make a PowerPoint presentation on the week’s topic or their progress on their project.
Instructor: M. Donohue
Area: Engineering, Natural Sciences

EN.540.636. Design: Pharmacokinetics/Dynamics. 3.00 Credits.

One semester overview of year long course, students that want a comprehensive understanding of pharmacokinetics and pharmacodynamics should take the 2 all 540.632 Projects in Design: Pharmacokinetics Spring 540.621 Projects in Design: Pharmacodynamics. This course covers the principles of pharmacokinetics and pharmacodynamics. Computer models ofpharmacokinetic and pharmacodynamics behavior will be developed and then used to design better drug delivery regimens and to analyze drug chemistry modifications.
Instructor: M. Donohue
Area: Engineering, Natural Sciences

EN.540.637. Application of Molecular Evolution to Biotechnology. 3.00 Credits.

One of the most promising strategies for successfully designing complex biomolecular functions is to exploit nature’s principles of evolution. This course provides an overview of the basics of molecular evolution as well as its experimental implementation. Current research problems in evolution-based biomolecular engineering will be used to illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), genetic circuits and complex biological systems including cells. A course in Biochemistry or Molecular Biology is recommended Meets with EN.540.437
Instructor: M. Ostermeier
Area: Engineering, Natural Sciences

EN.540.638. Advanced Topics in Pharmacokinetics and Pharmacodynamics I. 3.00 Credits.

This course involves a semester-long project in pharmacodynamics. Topics are chosen in consultation with instructor.
Prerequisites: EN.540.400 AND EN.540.421 OR EN.540.436
Instructor: M. Donohue
Area: Engineering, Natural Sciences

EN.540.639. Advanced Topics in Pharmacokinetics and Pharmacodynamics I. 3.00 Credits.

This course involves a semester-long project in pharmacodynamics. Topics are chosen in consultation with instructor.
Prerequisites: EN.540.400 AND EN.540.421 OR EN.540.436
Instructor: M. Donohue
Area: Engineering, Natural Sciences

EN.540.640. Micro/Nanotechnology: The Science and Engineering of Small Structures. 3.00 Credits.

The field of micro / nanotechnology has been gaining tremendous momentum as evidenced by an explosive rise in the number of publications, patents and commercial activities. This is an introductory course intended to expose students to the field as well as real world applications. Lectures will include an overview of scaling of material properties at the nanoscale, micro and nanofabrication methods and essential analytical tools of relevance to the field. All through the course, we will go over electronic, optical and biological applications of emerging micro and nanoscale devices and materials. Co-listed with EN.540.440.
Instructor: D. Gracias
Area: Engineering

EN.540.652. Advanced Transport Phenomena. 3.00 Credits.

It is the goal of this course to move the graduate student (and advanced undergraduate student) from the introductory level of transport phenomena (undergraduate) to a level that will allow them to be effective in researching transport-related topics in a variety of biomedical, chemical and biochemical engineering areas. The basic equations that govern mass, momentum, and energy transport will be derived and used to solve problems that demonstrate the physical insight necessary to apply these equations to original situations. Some topics include solution techniques utilizing expansions of harmonic functions, singularity solutions, lubrication theory for flow in confined geometries, boundary layer theory, Stokes flow, forced convection, buoyancy-driven flow, Taylor-Aris dispersion, and reaction-diffusion.
Instructor: K. Konstantopoulos
Area: Engineering

EN.540.660. Polymer Physics.

This course reviews current research problems in biomolecular design both from computational and experimental approaches. Current methods in structure prediction (folding, docking and design) will illustrate fundamental concepts in protein structure, biophysics, and optimization. Current research problems in evolution-based biomolecular engineering will illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), metabolic pathways, signaling pathways, genetic circuits and complex biological systems including cells. Students should have introductory training in Materials Science.
Instructor: Z. Xia
Area: Engineering, Natural Sciences

EN.540.661. Nanobioengineering Laboratory. 3.00 Credits.

Students explore different experimental methodologies in Nanobioengineering. Students work in small teams to complete one or more major projects expanding their understanding and applying their theoretical knowledge to practical problems. The course will employ a variety of experimental methods, from material synthesis to biological applications. Students report several times either orally and in writing on their accomplishments. Project meetings may be held outside of the appointed class time. Graduate students only
Instructor: A. Goffin
Area: Engineering

EN.540.662. Polymer Design and Bioconjugation. 3.00 Credits.

This course will focus on conventional to most recent inventions on polymer and conjugation chemistry. The weekly lectures will include the reaction strategy, designs and characterization techniques, structure-property relationship, simplistic approaches and versatile application oriented-solutions to Biomaterials and Tissue engineering related challenges. Students will learn how to devise creative strategies, process design and product development.
Instructor: A. Singh
Area: Engineering, Natural Sciences

EN.545.671. Advanced Thermodynamics in Practice. 3.00 Credits.

In this graduate level course, we will cover important principles in thermodynamics and kinetics along with examples relevant to engineering practice. After a short review of the first and second law of thermodynamics, we will move on to their application in engines and refrigeration. We will discuss the thermodynamic properties of systems consisting of pure species and mixtures, and address phase equilibria. With the key thermodynamic concepts in place, we will discuss topics in kinetics, including the fundamentals of reaction rates, rate laws, multiple reactions and non-elementary reaction kinetics. Finally, we will address how reactor type and properties, transport limitations, and phase equilibria influence reaction rate.
Instructor(s): TBA

EN.540.673. Advanced Chemical Reaction Engineering in Practice. 3.00 Credits.

Chemical reaction engineering deals with the analysis on data and the design of equipment in which reactions occur. Reactors may contain one or more phases and be used to conduct chemical or biochemical transformations. The course will cover the fundamental aspects of kinetics, data acquisition, data interpretation, heterogeneous catalysis and heat and mass transfer for each type of reactor. Special emphasis will be placed on the practical application of reaction engineering in the petrochemical, chemical, biochemical and materials industries. The course will make student aware of the needs and opportunities for chemical reaction engineering in industry.
Instructor: TBA
Writing Intensive.

EN.540.690. Chemical and Biomolecular Engineering Design. 3.00 Credits.

This course is one part of a two semester sequence in Chemical and Biomolecular Engineering Product Design. It is intended for students in the ChemBE master’s program. This course guides the student through the complex process of new product design. Product design concerns the recognition of customer needs, the creation of suitable specifications, and the selection of best products to fulfill needs. Students work in small teams to develop a new product idea, design the product and then iterate on prototype development. Students report several times both orally and in writing on their accomplishments. Time is allowed so that laboratory tests can be performed and/or prototypes can be built. Note that generally both courses, 540.609 and 540.610 must be taken to complete the prototype development. The two courses can be started in any term.
Instructor: M. Donohue
Area: Engineering

EN.670.619. Fundamental Physics and Chemistry of Nanomaterials. 3.00 Credits. (Cross Listed with the Institute for NanoBio Technology and Materials Science and Engineering)

This course will cover the physics and chemistry relevant to the design, synthesis, and characterization of nanoparticles. Topics include nanoparticle synthesis, functionalization, surface engineering, and applications in diagnostics and therapeutics. The properties of semiconductor quantum dots and magnetic nanoparticles will be reviewed along with techniques for nanoparticle manipulation, particle tracking, and bio-microrheology. Patterning tools including soft lithography, optical lithography, e-beam lithography, and template lithography will be discussed. Electron and scanning probe microscopy will be reviewed. Cross-listed with Materials Science & Engineering and Chemical & Biomolecular Engineering.
Instructor: Faculty.